Facing error during strarting cryosparc: "Could not get database status"

bhaskariicb · December 16, 2024, 6:32am

[dpatra@champ2 cryosparc_master]$ ./bin/cryosparcm restart
CryoSPARC is running.
Stopping cryoSPARC 
Shut down
Starting CryoSPARC System master process...
CryoSPARC is not already running.
configuring database...
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 47, in configure_mongo
    initialize_replica_set()
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 84, in initialize_replica_set
    admin_db = try_get_pymongo_db(mongo_client)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 251, in try_get_pymongo_db
    admin_db.command(({'serverStatus': 1}))
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/_csot.py", line 108, in csot_wrapper
    return func(self, *args, **kwargs)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 897, in command
    return self._command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 737, in _command
    return conn.command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 342, in inner
    return func(*args, **kwargs)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/pool.py", line 989, in command
    return command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/network.py", line 212, in command
    helpers._check_command_response(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 248, in _check_command_response
    raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {'operationTime': Timestamp(1734321702, 557), 'ok': 0.0, 'errmsg': 'there are no users authenticated', 'code': 13, 'codeName': 'Unauthorized', '$clusterTime': {'clusterTime': Timestamp(1734321702, 557), 'signature': {'hash': b'\x90\xcc%\xfdp\xdf+6@L\x11\xa4`+H\x9e\xd1\x82\x85\xab', 'keyId': 7447400517338136577}}}
[2024-12-16T09:31:47+05:30] Error configuring database. Most recent database log lines:
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten] git version: d352e6a4764659e0d0350ce77279de3c1f243e5c
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten] allocator: tcmalloc
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten] modules: none
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten] build environment:
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten]     distarch: x86_64
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten]     target_arch: x86_64
2024-12-16T09:31:34.285+0530 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_database" } }
2024-12-16T09:31:34.286+0530 E STORAGE  [initandlisten] Failed to set up listener: SocketException: Address already in use
2024-12-16T09:31:34.286+0530 I CONTROL  [initandlisten] now exiting
2024-12-16T09:31:34.286+0530 I CONTROL  [initandlisten] shutting down with code:48
[dpatra@champ2 cryosparc_master]$ whoami
dpatra
[dpatra@champ2 cryosparc_master]$ stat 
stat: missing operand
Try 'stat --help' for more information.
[dpatra@champ2 cryosparc_master]$ pwd 
/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master
[dpatra@champ2 cryosparc_master]$ stat /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master
  File: /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master
  Size: 4096      	Blocks: 8          IO Block: 4096   directory
Device: d61f715ah/3592384858d	Inode: 144118941659286048  Links: 13
Access: (0755/drwxr-xr-x)  Uid: ( 1868/  dpatra)   Gid: ( 4800/    iicb)
Access: 2024-12-16 09:31:20.000000000 +0530
Modify: 2024-12-13 16:10:52.000000000 +0530
Change: 2024-12-13 16:10:52.000000000 +0530
 Birth: 2024-12-13 15:09:58.000000000 +0530
[dpatra@champ2 cryosparc_master]$ hostname
champ2
[dpatra@champ2 cryosparc_master]$ grep HOSTNAME /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master
grep: /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master: Is a directory
[dpatra@champ2 cryosparc_master]$ grep HOSTNAME /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master
cryosparc_master/        cryosparc_master.tar.gz
[dpatra@champ2 cryosparc_master]$ grep HOSTNAME /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/config.sh 
export CRYOSPARC_MASTER_HOSTNAME="champ2"
export CRYOSPARC_FORCE_HOSTNAME=true
[dpatra@champ2 cryosparc_master]$ cryosparcm stop
-bash: cryosparcm: command not found
[dpatra@champ2 cryosparc_master]$ source /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/activate
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ cryosparcm stop
-bash: cryosparcm: command not found
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ which cryosparcm
/usr/bin/which: no cryosparcm in (/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin:/cm/local/apps/gcc/11.2.0/bin:/home/dpatra/.local/bin:/home/dpatra/bin:/cm/local/apps/environment-modules/4.5.3//bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/am/python/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.5.3/bin:/opt/pbs/bin:/opt/dell/srvadmin/bin)
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ find /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master -name cryosparcm
/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/bin/cryosparcm
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ export PATH=$PATH:/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/bin
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ cryosparcm stop 
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ps xww | grep -e cryosparc -e mongo
3735954 pts/66   S+     0:00 grep --color=auto -e cryosparc -e mongo
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ cryosparcm start
Starting CryoSPARC System master process...
^CTraceback (most recent call last):
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 33, in <module>
    sys.exit(load_entry_point('supervisor==4.2.5', 'console_scripts', 'supervisorctl')())
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 25, in importlib_load_entry_point

(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$     return next(matches).load()
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/importlib/metadata/__init__.py", line 171, in load
    module = import_module(match.group('module'))
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/supervisor/supervisorctl.py", line 40, in <module>
    from supervisor.options import ClientOptions
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/supervisor/options.py", line 13, in <module>
    import pkg_resources
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3292, in <module>
    def _initialize_master_working_set():
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3266, in _call_aside
    f(*args, **kwargs)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3304, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 591, in _build_master
    ws = cls()
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 584, in __init__
    self.add_entry(entry)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 640, in add_entry
    for dist in find_distributions(entry, True):
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2102, in find_on_path
    yield from factory(fullpath)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2159, in distributions_from_metadata
    if len(os.listdir(path)) == 0:
KeyboardInterrupt
^C
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ cryosparcm start
Starting CryoSPARC System master process...
CryoSPARC is not already running.
configuring database...
Warning: Could not get database status (attempt 1/3)
Warning: Could not get database status (attempt 2/3)
Warning: Could not get database status (attempt 3/3)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 47, in configure_mongo
    initialize_replica_set()
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 84, in initialize_replica_set
    admin_db = try_get_pymongo_db(mongo_client)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 251, in try_get_pymongo_db
    admin_db.command(({'serverStatus': 1}))
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/_csot.py", line 108, in csot_wrapper
    return func(self, *args, **kwargs)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 897, in command
    return self._command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/database.py", line 737, in _command
    return conn.command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 342, in inner
    return func(*args, **kwargs)
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/pool.py", line 989, in command
    return command(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/network.py", line 212, in command
    helpers._check_command_response(
  File "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/pymongo/helpers.py", line 248, in _check_command_response
    raise OperationFailure(errmsg, code, response, max_wire_version)
pymongo.errors.OperationFailure: there are no users authenticated, full error: {'operationTime': Timestamp(1734328759, 1), 'ok': 0.0, 'errmsg': 'there are no users authenticated', 'code': 13, 'codeName': 'Unauthorized', '$clusterTime': {'clusterTime': Timestamp(1734328759, 1), 'signature': {'hash': b';k\xf4{"\xe6\x8f\xc2P\xb2Q\xf3\xe1\x13g\xbfQ\xb9(\x9b', 'keyId': 7447400517338136577}}}
[2024-12-16T11:29:28+05:30] Error configuring database. Most recent database log lines:
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten] git version: d352e6a4764659e0d0350ce77279de3c1f243e5c
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten] allocator: tcmalloc
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten] modules: none
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten] build environment:
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten]     distarch: x86_64
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten]     target_arch: x86_64
2024-12-16T11:29:14.976+0530 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/scratch/dpatra/cryosparcuser/cryosparc/cryosparc_database" } }
2024-12-16T11:29:14.977+0530 E STORAGE  [initandlisten] Failed to set up listener: SocketException: Address already in use
2024-12-16T11:29:14.977+0530 I CONTROL  [initandlisten] now exiting
2024-12-16T11:29:14.977+0530 I CONTROL  [initandlisten] shutting down with code:48
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ps xww | grep -e cryosparc -e mongo
3740520 ?        Ss     0:00 python /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/supervisord.conf
3742262 pts/66   S+     0:00 grep --color=auto -e cryosparc -e mongo
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$

wtempel · December 16, 2024, 4:05pm

Please can you post the outputs of these commands:

uname -a
ps -eo user:12,pid,ppid,start,command | grep -e cryosparc_ -e mongo
ls -l /tmp/cryosparc*.sock /tmp/mongo*.sock
sudo ss -anp | grep 39001  | sed "s/\s\+/ /g"

bhaskariicb · December 17, 2024, 5:38am

(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ uname -a
Linux champ2 4.18.0-425.3.1.el8.x86_64 #1 SMP Fri Sep 30 11:45:06 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ps -eo user:12,pid,ppid,start,command | grep -e cryosparc_ -e mongo
saikatc       360290       1 15:12:41 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/saikatc/cryosparc/cryosparc_master/supervisord.conf
saikatc       360602  360290 15:12:46 mongod --auth --dbpath /home/saikatc/cryosparc/cryosparc_database --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
saikatc       360842  360290 15:12:50 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       360969  360842 15:12:54 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361248  360290 15:13:00 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361269  361248 15:13:00 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361304  360290 15:13:01 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361339  361304 15:13:02 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613432       1   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/janesh/cryosparc/cryosparc_master/supervisord.conf
janesh        613652  613432   Nov 14 mongod --auth --dbpath /home/janesh/cryosparc/cryosparc_database --port 45001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
janesh        613839  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:45002 cryosparc_command.command_core:start() -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613858  613839   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:45002 cryosparc_command.command_core:start() -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613996  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:45003 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614003  613996   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:45003 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614050  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:45005 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614053  614050   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:45005 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614173  613432   Nov 14 /home/janesh/cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
saikatc      3090683  360290 10:57:32 /home/saikatc/cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
dpatra       3090936 3447925 10:57:33 grep --color=auto -e cryosparc_ -e mongo
dpatra       3740520       1 11:29:04 python /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/supervisord.conf
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ls -l /tmp/cryosparc*.sock /tmp/mongo*.sock
srwx------ 1 dpatra  iicb 0 Dec 16 11:29 /tmp/cryosparc-supervisor-2f68d8c089c73f0f3ce17dc044108e4f.sock
srwx------ 1 saikatc ccmb 0 Dec 16 15:12 /tmp/cryosparc-supervisor-c140516694fc079dfff3deaf5b3ede47.sock
srwx------ 1 saikatc ccmb 0 Dec 16 15:12 /tmp/mongodb-39001.sock
srwx------ 1 janesh  ccmb 0 Nov 14 18:43 /tmp/mongodb-45001.sock
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ sudo ss -anp | grep 39001  | sed "s/\s\+/ /g"

We trust you have received the usual lecture from the local System
Administrator. It usually boils down to these three things:

    #1) Respect the privacy of others.
    #2) Think before you type.
    #3) With great power comes great responsibility.

[sudo] password for dpatra: 
dpatra is not in the sudoers file.  This incident will be reported.
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ 
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ uname -a
Linux champ2 4.18.0-425.3.1.el8.x86_64 #1 SMP Fri Sep 30 11:45:06 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ps -eo user:12,pid,ppid,start,command | grep -e cryosparc_ -e mongo
saikatc       360290       1 15:12:41 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/saikatc/cryosparc/cryosparc_master/supervisord.conf
saikatc       360602  360290 15:12:46 mongod --auth --dbpath /home/saikatc/cryosparc/cryosparc_database --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
saikatc       360842  360290 15:12:50 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       360969  360842 15:12:54 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361248  360290 15:13:00 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361269  361248 15:13:00 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361304  360290 15:13:01 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
saikatc       361339  361304 15:13:02 python /home/saikatc/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/saikatc/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613432       1   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/janesh/cryosparc/cryosparc_master/supervisord.conf
janesh        613652  613432   Nov 14 mongod --auth --dbpath /home/janesh/cryosparc/cryosparc_database --port 45001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
janesh        613839  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:45002 cryosparc_command.command_core:start() -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613858  613839   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:45002 cryosparc_command.command_core:start() -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        613996  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:45003 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614003  613996   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:45003 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614050  613432   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:45005 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614053  614050   Nov 14 python /home/janesh/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:45005 -c /home/janesh/cryosparc/cryosparc_master/gunicorn.conf.py
janesh        614173  613432   Nov 14 /home/janesh/cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
saikatc      3090683  360290 10:57:32 /home/saikatc/cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
dpatra       3090936 3447925 10:57:33 grep --color=auto -e cryosparc_ -e mongo
dpatra       3740520       1 11:29:04 python /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /scratch/dpatra/cryosparcuser/cryosparc/cryosparc_master/supervisord.conf
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ ls -l /tmp/cryosparc*.sock /tmp/mongo*.sock
srwx------ 1 dpatra  iicb 0 Dec 16 11:29 /tmp/cryosparc-supervisor-2f68d8c089c73f0f3ce17dc044108e4f.sock
srwx------ 1 saikatc ccmb 0 Dec 16 15:12 /tmp/cryosparc-supervisor-c140516694fc079dfff3deaf5b3ede47.sock
srwx------ 1 saikatc ccmb 0 Dec 16 15:12 /tmp/mongodb-39001.sock
srwx------ 1 janesh  ccmb 0 Nov 14 18:43 /tmp/mongodb-45001.sock
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$ sudo ss -anp | grep 39001  | sed "s/\s\+/ /g"

We trust you have received the usual lecture from the local System
Administrator. It usually boils down to these three things:

    #1) Respect the privacy of others.
    #2) Think before you type.
    #3) With great power comes great responsibility.

[sudo] password for dpatra: 
dpatra is not in the sudoers file.  This incident will be reported.
(cryosparc_master_env) [dpatra@champ2 cryosparc_master]$

I don’t have the permission to check the network connections on port 39001

wtempel · December 17, 2024, 2:36pm

At least two CryoSPARC instances, in addition to your own, are running on this computer. One of the additional CryoSPARC instances appears to have been configured with the same --port 39000 parameter (which might be used by default when no ./cryosparc_master/install.sh --port is specified).
The installation of multiple CryoSPARC master instances on the same computer must be coordinated carefully. The 10-port ranges beginning at the install.sh --port parameter (a.k.a. CRYOSPARC_BASE_PORT defined inside cryosparc_master/config.sh) must not overlap. May I suggest

Ensure all users who might install CryoSPARC on this computer are aware of the restriction.
A coordinator should track port ranges in use and assign a unique and unused continuous range of 10 network ports to anyone installing a CryoSPARC instance. Users installing CryoSPARC should use the install.sh --port parameter to avoid duplicate use of the default port range. When selecting/assigning a port range, one may want to
- avoid ports below the number shown by the command
```
cat /proc/sys/net/ipv4/ip_unprivileged_port_start
```
- avoid ports withhin the range shown by the command
```
cat /proc/sys/net/ipv4/ip_local_port_range
```
- avoid ports used by other users or software on the computer
If appropriate, change the port range of a CryoSPARC instance with the command
```
cryosparcm changeport 9000
```
where 9000 should be replaced with the number at the start of a suitable port range.

bhaskariicb · December 20, 2024, 6:41am

Thank You. Now it is working after changing the port.